The flowsim package

Provides clonesim, a clone simulator that simulates shotgun
genomic clones, and flowsim, that takes the output from clonesim
(or any other Fasta-formatted file) and generates simulated
reads from them mimicing Roche's 454 pyrosequencing technology,
writing output in 454's native SFF format. The flowgram
generation is based on empirical distributions derived from real
data (although analytic distributions are available too, if you
prefer).